Bin quality
#Generate quality biplot
bin_metadata %>%
select(genome,completeness,contamination,overall_strategy, assembly, size) %>%
ggplot(aes(x=completeness,y=contamination,size=size,color=overall_strategy)) +
geom_point(alpha=0.3, size=1.5) +
scale_color_manual(values=strategy_colors)+
ylim(c(10,0)) +
labs(y= "Contamination", x = "Completeness") +
theme_classic() +
theme(legend.position = "none")
bin_metadata %>%
select(genome,completeness,contamination,overall_strategy, assembly, size) %>%
mutate(assembly=factor(assembly,levels=assemblies)) %>%
ggplot(aes(y=completeness,x=overall_strategy, group=overall_strategy, color=overall_strategy)) +
geom_jitter(alpha=0.1)+
geom_boxplot(outlier.shape = NA)+
scale_color_manual(values=strategy_colors)+
facet_grid(~assembly, space = "free", scale="free")+
labs(x = "Strategies", y="Completeness") +
theme_classic() +
theme(legend.position = "none")
bin_metadata %>%
select(genome,completeness,contamination,overall_strategy, assembly, size) %>%
ggplot(aes(x=completeness,color=assembly)) +
geom_density(alpha=0.3, size=1.5, linewidth=1) +
scale_color_manual(values=assembly_colors)+
labs(x = "Completeness", y="Density") +
theme_classic()
bin_metadata %>%
select(genome,completeness,contamination,overall_strategy, assembly, size) %>%
mutate(assembly=factor(assembly,levels=assemblies)) %>%
ggplot(aes(y=contamination,x=overall_strategy, group=overall_strategy, color=overall_strategy)) +
geom_jitter(alpha=0.1)+
geom_boxplot(outlier.shape = NA)+
scale_color_manual(values=strategy_colors)+
facet_grid(~assembly, space = "free", scale="free")+
labs(x = "Strategies", y="Contamination") +
theme_classic() +
theme(legend.position = "none")
bin_metadata %>%
select(genome,completeness,contamination,assembly, size) %>%
ggplot(aes(x=contamination,color=assembly,)) +
geom_density(alpha=0.3, size=1.5, linewidth=1) +
scale_color_manual(values=assembly_colors)+
labs(x = "Contamination", y="Density") +
theme_classic()
